The PANOPTES router provides a local network within the unit, to which both Rasbery Pis connect, and to which you can connect to drive/test the unit. The router has a single connection to the outside: this is the connection to your university network. Whichever way you wire the internal network within the PANOPTES unit, you will need this connection to the outside. From the university network, you should only need a single connection point to the router.
I hope this helps -